Specimen Collection


Special collection materials and transport media are available in Room 5.175 McCullough Building. When the laboratory is closed, they may be obtained from Microbiology Specimen Receiving, Room 5.137 McCullough. Specimens must be collected as soon as possible after the onset of illness. Culture specimens should be immediately transported to the laboratory on ice to insure virus viability. Specify suspected viral agents on request slip.

Direct Viral Antigen Detection

Rapid Direct Viral Antigen Detection for Respiratory Specimens

Viral culture can detect most of the viral agents associated with respiratory disease but may require several days to a week to become positive. Direct detection of viral agents using rapid test methods, i.e. immunofluorescent stains or enzyme-linked assays, can dramatically speed detection of specific viral agents.

The most critical factor in the direct detection of respiratory viruses is collection of a proper specimen containing adequate numbers of infected cells. The specimen of choice is a nasal wash.

Collection of a Nasal Wash:

  1. Materials: 5 mL phosphate buffered saline (PBS); Rubber bulb (30 mL ear syringe)
  2. Aspirate the PBS into the bulb. Tilt the tube. Use all the PBS. For young infants, use 3-5 mL. Empty the tube of excess PBS to avoid diluting the specimen.
  3. Hold the patient's face chin up. A sitting position will work best. Fit the tip of the bulb into a nostril.
  4. Quickly squeeze the bulb. Immediately aspirate the PBS back into the bulb.
  5. Transfer the specimen back to the empty PBS tube. Label the tube.
  6. Transport the specimen on ice. Place the specimen in the ice bucket.
  7. Return the rubber bulb to the holding area or laboratory along with the specimen.

External Lesions - Herpes simplex virus or Varicella zoster

  1. Select a fresh vesicle (<3 days old). Scabs, vesicular fluid, bloody specimens, or pus are unsatisfactory for FA examination.
  2. Incise the vesicle peripherally with the beveled edge of a sterile needle and gently lift back the top of the vesicle.
  3. Blot the excess fluid with a sterile culturette swab and submit for virus isolation in viral transport medium (M4).
  4. Roughly scrape the base of the lesion with the scalpel blade to obtain epithelial cells. Do not induce bleeding. It is important to obtain a sufficient quantity of basal epithelial cells.
  5. Thinly spread the collected material over the 2 wells and label the slide with patient's name. Allow to air dry.
  6. Place the slide in slide holder provided and label with the patient's name and UT number.
  7. Transport to the laboratory along with the specimen for culture. A culture backup is required for HSV.

Table of infections and common virus/agent involved with suggested specimens.

Infection and Common Virus/Agent Involved Suggested Specimens
Arboviruses Routine culture not available; serologies suggested.
Coxsackie A and B Throat swab, stool/rectal swab
EBV Routine culture not available; serologies suggested.
Rubella NP swab, urine
Central Nervous System
Arboviruses Routine culture not available; serologies suggested.
Enteroviruses Throat, stool/rectal swab, CSF
Herpes simplex (HSV) CSF, vesicle fluid, brain tissue (temporal lobe)
Influenza Nasal secretion/washing, throat
LCM Routine culture not available; serologies suggested.
Mumps Throat, CSF, urine
Congenital infection
CMV Urine, blood (4 mL/7 mL), throat
Herpes simplex Vesicle fluid, throat, eye, CSF
Rubella NP swab, urine, throat
CMV Blood-buffy coat (7 mL/EDTA purple-topped tube), urine, bronchoalveolar lavage (BAL), lung, throat, sputum, trach suction, bronch brush/wash
Enteroviruses Throat, stool/rectal swab
Measles Throat, NP swab, blood (7 mL green-topped tube)
Rubella NP swab, throat
Coxsackie A Throat, stool/rectal swab, vesicle fluid
Herpes simplex (HSV) Vesicle fluid/swab
Varicella-zoster (VZ) Vesicle fluid/swab
Eye infections, conjunctivitis
Adenovirus Conjunctival swab (culture)
Chlamydia trachomatis Conjunctival swab (culture), slide (DFA)
Herpes simplex (HSV) Conjunctival swab, corneal scraping
Varicella-zoster (VZ) Conjunctival swab, corneal scraping
Gastrointestinal syndromes
Enteroviruses Stool/rectal swab
Adenovirus 40/41 Stool/rectal swab
Adenoviruses Stool/rectal swab
Rotavirus Stool/rectal swab
CMV Blood (2-7 mL EDTA, purple top), urine, throat
EBV Routine culture not available; serologies suggested.
HAV Routine culture not available; serologies suggested.
HBV Routine culture not available; serologies suggested.
Immunocompromised patients
CMV See "CMV" specimen list.
EBV Routine culture not available; serologies suggested.
HAV Routine culture not available; serologies suggested.
Herpes simplex (HSV) Throat, vesicle fluid/swab
Varicella-zoster (VZ) Vesicle fluid/swab
CMV Throat, urine, blood (2-7 mL/EDTA, purple-topped tube)
EBV Routine culture not available; serologies suggested.
Mycocarditis, pericarditis
Coxsackie A and B Throat swab, stool/rectal swab
Echovirus Swab, pericardial fluid/tissue
Respiratory Syndromes
Adenoviruses Throat, NP swab
Cytomegalovirus (CMV) See "CMV" specimen list
Enteroviruses Nasal washing/secretion, throat
Influenza Nasal washing/secretion, throat or NP swab, sputum
Mumps Throat or NP swab, urine, serology
Parainfluenza Nasal washing/secretion, NP swab, throat
Rhinovirus Nasal or NP swab
RSV Nasal washing/secretion